Up: Components summary Author

Katherine Icay

Component Version Inputs Outputs Description
AnnotEnsembl 1.0 annot Takes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome.
AnnotMirbase 1.0 annot Takes a GFF3 file downloaded from miRBase and modifies the genomic locations to reference by Ensembl transcript ID (instead of chromosome) and relative positions inside the transcript ID (start and end positions).
Bam2Fastq 0.1 in out Revert BAM file to Fastq file for realignment.
CreateSQLiteDB 0.1 DBlist Create miRNA-target gene database(s) for fast and simple SQLite query of potentially interesting regulatory pairs.
CreateSQLiteIDs 0.1 geneList wIDs For a subset of genes, create a file with additional reference IDs.
CSVColRename 0.1 in, reference out Changes column names in a CSV file given a reference file.
DataOverlap 1.0 annot1, annot2 annot Take the union of and collapse 2 datasets, with the option to filter out rows with NAs.
DEan 0.4 expr, treatment array, diffExpr Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test.
ExpressionStats 0.1 expr, ref, geneSet, bodyMap stats, statsArray, report Given an expression matrix and a CSV containing sample IDs and treatment groups, calculate basic statistics by treatment group: mean, median, and standard deviation of genes.
ExpressionSubset 0.1 exprMatrix, reference subset Given an expression matrix and a CSV containing a subset of interest in one column (e.g.
ExprTableReport 1.0 expr, ref, colLabels, annotation, geneSet, bodyMap table, expressed, document, report

Generates expression statistics into an HTML report.

ExtractCond 0.1 exprMatrix, reference table Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file.
GlobalCorrelation 1.2 gene, mirna correlated_filtered, correlated_all, expression_miRNA, expression_mRNA Compute correlation between miRNA and gene/transcript expression.
HTSeqCount 1.0 bam, annotation_mirbase counts Quantify reads mapped to EnsemblID transcripts for a given sample.
HTSeqExprMatrix 0.1 samples, TPM countArray, no_feature Takes a CSV list of outputs from HTSeqCount to merge into an expression matrix.
HTSeqExprNormalize 0.1 expr array Takes as input "raw", integer count expression matrix of quantified sequenced reads and outputs a scale-normalised, log-transformed expression matrix.
NCRNAAnnot 1.0 expression, gtf annotated Creates reference files for gene features and known ncRNAs and creates additional columns for a putatively novel miRNA expression matrix with information on relative genomic location (e.g. intragenic/intergenic, host gene and transcript) and neighbouring or overlapping ncRNAs.
NovelExprMatrix 1.0 novelArray csv, csv_wID Take output of miRanalyzer (or miRDeep2) and create an expression matrix with the putative novel miRNAs found.
NovelMatureSeq 0.1 novel, fqFiles mature, array Given a set of putative novel miRNA regions (e.g. output from miRanalyzer or miRDeep2), retrieves consensus functional "mature" region that can then be used for predicting target genes (e.g. as input to MirMatch.
NovelMirnas 1.0 fqFiles, mirDP_genome, mirDP_mature, mirDP_related_mature, mirDP_precursor array Performs novel miRNA discovery using miRanalyzer or mirDeep2, depending on what is installed and what you want to use.
SmallRNAPrep 1.0 reads fastq, stats Uses FASTX-Toolkit to perform adapter trimming, artifact filtering, base-quality filtering, and read trimming for single-end read data.
SmallRNAQC 1.0 reads, mates, stats, bam, mergeStats qc, report, fastqc Performs all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines.
TPquery 0.3 refTable array, annot Retrieve target prediction and target validated data from an SQLite database to annotate a list of miRNAs or a list of miRNA-target gene pairs.

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